Dear all,

1. I want to generate gromacs topology with force field parameters
from SMILES. RDKit has two FFs so this should be easy task at least for
this two force fields. Bond and angle parameters can be simply take
from Get*BondStretchParams and Get*StretchBendParams, but vdW and
torsian parameters are not so obvious.
-) How to assign vdW params to atoms? How can I extract this from rdkit?
-) How to convert result of Get*TorsionParams (Inversion and OopBend) to
something which can be used by gromacs? (I know, it is not strictly
question about RDKit)

2. It think I found bug in MMFF implementation:

>>> acetona=Chem.AddHs(Chem.MolFromSmiles('[CH2-]C(=O)C') )
>>> AllChem.MMFFHasAllMoleculeParams(acetona)
>>> acetmm=AllChem.MMFFGetMoleculeProperties(acetona)
>>> sumch=0
>>> for i in range( len(acetona.GetAtoms()) ):
...  sumch+=acetmm.GetMMFFPartialCharge(i)
>>> round(sumch,2)
>>> for i in range( len(acetona.GetAtoms()) ):
...  sumch+=acetmm.GetMMFFFormalCharge(i)
>>> round(sumch,2)

The molecule is anion but sum of formal or partial charge is zero. In
my opinion it is not currect result :) The same behaviour I also
observed for other exotic C-anion.



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